Biogeography and evolution of Thermococcus isolates from hydrothermal vent systems of the Pacific.

Price MT, Fullerton H, Moyer CL - Front Microbiol (2015)

Bottom Line:
The biodiversity identified in Thermococcus isolates and presence of distinct lineages within the same vent site suggests the utilization of varying ecological niches in this genus.In addition to resolving biogeographic patterns in Thermococcus, this study has raised new questions about the closely related Pyrococcus genus.The phylogenetic placement of Pyrococcus type strains shows the close relationship between Thermococcus and Pyrococcus and the unresolved divergence of these two genera.

Affiliation: Department of Biology, Western Washington University Bellingham, WA, USA.

ABSTRACTThermococcus is a genus of hyperthermophilic archaea that is ubiquitous in marine hydrothermal environments growing in anaerobic subsurface habitats but able to survive in cold oxygenated seawater. DNA analyses of Thermococcus isolates were applied to determine the relationship between geographic distribution and relatedness focusing primarily on isolates from the Juan de Fuca Ridge and South East Pacific Rise. Amplified fragment length polymorphism (AFLP) analysis and multilocus sequence typing (MLST) were used to resolve genomic differences in 90 isolates of Thermococcus, making biogeographic patterns and evolutionary relationships apparent. Isolates were differentiated into regionally endemic populations however there was also evidence in some lineages of cosmopolitan distribution. The biodiversity identified in Thermococcus isolates and presence of distinct lineages within the same vent site suggests the utilization of varying ecological niches in this genus. In addition to resolving biogeographic patterns in Thermococcus, this study has raised new questions about the closely related Pyrococcus genus. The phylogenetic placement of Pyrococcus type strains shows the close relationship between Thermococcus and Pyrococcus and the unresolved divergence of these two genera.

Figure 3: Maximum likelihood phylogenetic tree of the SSU rRNA with the inclusion of Palaeococcus species and with Staphylothermus marinus as an outgroup. Clade I is ancestral to both Pyrococcus type strains and Thermococcus isolates in clades II–X. Numbers at nodes represent bootstrap values.

Mentions:
The ML tree for the SSU rRNA gene, which includes Palaeococcus isloates and is rooted with Staphylothermus marinus, places the Clade I Thermococcus isolates in an ancestral position to Pyrococcus type strains and the Thermococcus isolates found in Clades II through X (Figure 3). This illustrates the paraphyletic associations among members of the Thermococcus and Pyrococcus genera. Several other Crenarchaeota were tested as an outgroup including: Cenarchaeum symbiosum, Sulfolobus tokodaii, Nitrosopumilus maritimus, and Pyrobaculum aerophilum. None of these other taxa changed the position of the root (data not shown).

Figure 3: Maximum likelihood phylogenetic tree of the SSU rRNA with the inclusion of Palaeococcus species and with Staphylothermus marinus as an outgroup. Clade I is ancestral to both Pyrococcus type strains and Thermococcus isolates in clades II–X. Numbers at nodes represent bootstrap values.

Mentions:
The ML tree for the SSU rRNA gene, which includes Palaeococcus isloates and is rooted with Staphylothermus marinus, places the Clade I Thermococcus isolates in an ancestral position to Pyrococcus type strains and the Thermococcus isolates found in Clades II through X (Figure 3). This illustrates the paraphyletic associations among members of the Thermococcus and Pyrococcus genera. Several other Crenarchaeota were tested as an outgroup including: Cenarchaeum symbiosum, Sulfolobus tokodaii, Nitrosopumilus maritimus, and Pyrobaculum aerophilum. None of these other taxa changed the position of the root (data not shown).

Bottom Line:
The biodiversity identified in Thermococcus isolates and presence of distinct lineages within the same vent site suggests the utilization of varying ecological niches in this genus.In addition to resolving biogeographic patterns in Thermococcus, this study has raised new questions about the closely related Pyrococcus genus.The phylogenetic placement of Pyrococcus type strains shows the close relationship between Thermococcus and Pyrococcus and the unresolved divergence of these two genera.

Affiliation:
Department of Biology, Western Washington University Bellingham, WA, USA.

ABSTRACTThermococcus is a genus of hyperthermophilic archaea that is ubiquitous in marine hydrothermal environments growing in anaerobic subsurface habitats but able to survive in cold oxygenated seawater. DNA analyses of Thermococcus isolates were applied to determine the relationship between geographic distribution and relatedness focusing primarily on isolates from the Juan de Fuca Ridge and South East Pacific Rise. Amplified fragment length polymorphism (AFLP) analysis and multilocus sequence typing (MLST) were used to resolve genomic differences in 90 isolates of Thermococcus, making biogeographic patterns and evolutionary relationships apparent. Isolates were differentiated into regionally endemic populations however there was also evidence in some lineages of cosmopolitan distribution. The biodiversity identified in Thermococcus isolates and presence of distinct lineages within the same vent site suggests the utilization of varying ecological niches in this genus. In addition to resolving biogeographic patterns in Thermococcus, this study has raised new questions about the closely related Pyrococcus genus. The phylogenetic placement of Pyrococcus type strains shows the close relationship between Thermococcus and Pyrococcus and the unresolved divergence of these two genera.